ArticleFrontiers in microbiology2021
Comparison of Current Methods for Signal Peptide Prediction in Phytoplasmas.
Article in Frontiers in microbiology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 25 citations in OpenAlex.
- Phytoplasma-plant interactions: effector-mediated host reprogramming, hormonal crosstalk, metabolic alterations and plant-mediated vector manipulation.World journal of microbiology & biotechnology · 2026Review
- Hl48 modulates argonaute 2 to enhance RNA interference in ticks.Frontiers in cellular and infection microbiology · 2026Article
- Effector innovation in genome-reduced phytoplasmas and other host-dependent mollicutes.PLoS genetics · 2025Article
- Definition of the effector landscape across 13 phytoplasma proteomes with LEAPH and EffectorComb.NAR genomics and bioinformatics · 2024Article
- Phytoplasma: A plant pathogen that cannot be ignored in agricultural production-Research progress and outlook.Molecular plant pathology · 2024Review
- DeTox: a pipeline for the detection of toxins in venomous organisms.Briefings in bioinformatics · 2024Article
- Exploring the secretome ofFrontiers in bioengineering and biotechnology · 2024Article
- Antimicrobial peptides in Dendrobium officinale: Genomic parameters, peptide structures, and gene expression patterns.The plant genome · 2023Article
- A Novel R2R3-MYB Transcription FactorInternational journal of molecular sciences · 2022Article
- Putative Protein Discovery from Microalgal Genomes as a Synthetic Biology Protein Library for Heavy Metal Bio-Removal.Biology · 2022Article
- The Complete Genome of the "Flavescence Dorée" Phytoplasma Reveals Characteristics of Low Genome Plasticity.Biology · 2022Article
- Phytoplasma effector Zaofeng6 induces shoot proliferation by decreasing the expression of ZjTCP7 in Ziziphus jujuba.Horticulture research · 2022Article
- Recent Advances in the Prediction of Subcellular Localization of Proteins and Related Topics.Frontiers in bioinformatics · 2022Review
- Accelerating Complete Phytoplasma Genome Assembly by Immunoprecipitation-Based Enrichment and MinION-Based DNA Sequencing for Comparative Analyses.Frontiers in microbiology · 2021Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Although phytoplasma studies are still hampered by the lack of axenic cultivation methods, the availability of genome sequences allowed dramatic advances in the characterization of the virulence mechanisms deployed by phytoplasmas, and highlighted the detection of signal peptides as a crucial step to identify effectors secreted by phytoplasmas. However, various signal peptide prediction methods have been used to mine phytoplasma genomes, and no general evaluation of these methods is available so far for phytoplasma sequences. In this work, we compared the prediction performance of SignalP versions 3.0, 4.0, 4.1, 5.0 and Phobius on several sequence datasets originating from all deposited phytoplasma sequences. SignalP 4.1 with specific parameters showed the most exhaustive and consistent prediction ability. However, the configuration of SignalP 4.1 for increased sensitivity induced a much higher rate of false positives on transmembrane domains located at N-terminus. Moreover, sensitive signal peptide predictions could similarly be achieved by the transmembrane domain prediction ability of TMHMM and Phobius, due to the relatedness between signal peptides and transmembrane regions. Beyond the results presented herein, the datasets assembled in this study form a valuable benchmark to compare and evaluate signal peptide predictors in a field where experimental evidence of secretion is scarce. Additionally, this study illustrates the utility of comparative genomics to strengthen confidence in bioinformatic predictions.
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